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318 12 Building Bioinformatics Ontologies

any additions or modifications to the ontology.

Summary

• Ontology validation consists of the following activities:
  
  
  1. Verify the fulfillment of the purpose.
  
  
  2. Check that all usage examples are expressible.
  
  
  3. Create examples that are consistent with the ontology, and determine
     whether they are meaningful.
  
  
  4. Check that the ontology is formally consistent.
  
  
  
  


• Ontologies evolve over time due to changing requirements and circum-
  stances.

12.9 Exercises

Most of the exercises are based on the development of an ontology for single

nucleotide polymorphism (SNP).

1. The informal description of the purpose of the SNP ontology is the follow-
   ing:A small group of researchers would like to formalize their understanding of
   single nucleotide polymorphisms. The ontology will only be used for a few weeks.
   The ontology is only concerned with giving a high-level view of SNPs, which
   does not deal with the details.
   Summarize the purpose succinctly in a table as in section 12.1.


2. Add consistency checking to the use case diagram in figure 12.1 for the
   medical chart ontology.


3. Choose an ontology language for the SNP ontology, and give a design
   rationale for your choice.


4. There already exist ontologies that deal with SNPs. For example, the SNP
   database (SNPdb) ontology in (Niu et al. 2003) is written in OWL and
   gives detailed information about the methods for finding SNPs. Is it ap-
   propriate to reuse SNPdb by importing it?


5. Build a concept hierarchy for the SNP ontology.